Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells

Demeter, Amanda, Jacomin, Anne-Claire, Gul, Lejla, Lister, Ashleigh, Lipscombe, James, Invernizzi, Rachele, Branchu, Priscilla, Macaulay, Iain, Nezis, Ioannis P., Kingsley, Robert A. ORCID:, Korcsmaros, Tamas and Hautefort, Isabelle (2022) Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Frontiers in Cellular and Infection Microbiology, 12. ISSN 2235-2988

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Macroautophagy is a ubiquitous homeostasis and health-promoting recycling process of eukaryotic cells, targeting misfolded proteins, damaged organelles and intracellular infectious agents. Some intracellular pathogens such as Salmonella enterica serovar Typhimurium hijack this process during pathogenesis. Here we investigate potential protein-protein interactions between host transcription factors and secreted effector proteins of Salmonella and their effect on host gene transcription. A systems-level analysis identified Salmonella effector proteins that had the potential to affect core autophagy gene regulation. The effect of a SPI-1 effector protein, SopE, that was predicted to interact with regulatory proteins of the autophagy process, was investigated to validate our approach. We then confirmed experimentally that SopE can directly bind to SP1, a host transcription factor, which modulates the expression of the autophagy gene MAP1LC3B. We also revealed that SopE might have a double role in the modulation of autophagy: Following initial increase of MAP1LC3B transcription triggered by Salmonella infection, subsequent decrease in MAP1LC3B transcription at 6h post-infection was SopE-dependent. SopE also played a role in modulation of the autophagy flux machinery, in particular MAP1LC3B and p62 autophagy proteins, depending on the level of autophagy already taking place. Upon typical infection of epithelial cells, the autophagic flux is increased. However, when autophagy was chemically induced prior to infection, SopE dampened the autophagic flux. The same was also observed when most of the intracellular Salmonella cells were not associated with the SCV (strain lacking sifA) regardless of the autophagy induction status before infection. We demonstrated how regulatory network analysis can be used to better characterise the impact of pathogenic effector proteins, in this case, Salmonella. This study complements previous work in which we had demonstrated that specific pathogen effectors can affect the autophagy process through direct interaction with autophagy proteins. Here we show that effector proteins can also influence the upstream regulation of the process. Such interdisciplinary studies can increase our understanding of the infection process and point out targets important in intestinal epithelial cell defense.

Item Type: Article
Additional Information: Funding Information: The work of AD, RI, TK and IH were supported by the UKRI BBSRC Gut Microbes and Health Institute Strategic Programme BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10355 as well as a BBSRC Core Strategic Programme Grant for Genomes to Food Security (BB/CSP1720/1) and its constituent work packages, BBS/E/T/000PR9819 and BBS/E/T/000PR9817. LG was supported by a BBSRC - Norwich Research Park Biosciences Doctoral Training Partnership grant (BB/M011216/1). RK was supported by research grants BB/N007964/1 and BB/M025489/1, and by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent projects BBS/E/F/000PR10348 and BBS/E/F/000PR10349. ACJ and IPN were supported by BBSRC grants BB/L006324/1 and BB/P007856/1.
Uncontrolled Keywords: autophagy,host-microbe interactions,map1lc3b,network biology,salmonella typhimurium,sope,microbiology,immunology,microbiology (medical),infectious diseases,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2400/2404
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 02 Nov 2022 09:30
Last Modified: 28 Mar 2023 09:30
DOI: 10.3389/fcimb.2022.834895


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